chr10-57387016-T-C

Variant names:

• chr10-57387016-T-C
• rs2928445
• ENST00000812047.1:n.75+20221A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000812047.1(ENSG00000305625):​n.75+20221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,904 control chromosomes in the GnomAD database, including 5,979 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (5979 hom., cov: 29)
• Consequence: ENSG00000305625 ENST00000812047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 4 publications found

Genes affected

ENSG00000305625 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812047.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305625	ENST00000812047.1		n.75+20221A>G		intron	N/A
	ENSG00000305625	ENST00000812048.1		n.63-10910A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33221 AN: 151786 Hom.: 5972 Cov.: 29

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.191

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.219 AC: 33273 AN: 151904 Hom.: 5979 Cov.: 29 AF XY: 0.220 AC XY: 16371 AN XY: 74252

African (AFR) AF: 0.482 AC: 19912 AN: 41344

American (AMR) AF: 0.262 AC: 3997 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 290 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5164

South Asian (SAS) AF: 0.234 AC: 1125 AN: 4810

European-Finnish (FIN) AF: 0.0643 AC: 681 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0828 AC: 5628 AN: 67968

Other (OTH) AF: 0.192 AC: 406 AN: 2116

Alfa AF: 0.134 Hom.: 2954

Bravo AF: 0.245

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.76
PhyloP100		-0.93

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2928445; hg19: chr10-59146776;